3T81

Crystal Structure of diiron adenine deaminase

PDB DOI: https://doi.org/10.2210/pdb3T81/pdb

Classification: HYDROLASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-01 Released: 2011-11-02
Deposition Author(s): Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.287
R-Value Work: 0.185
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of diiron adenine deaminase

Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 130.47 kDa
Atom Count: 8,674
Modelled Residue Count: 1,166
Deposited Residue Count: 1,216
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine deaminase 2	A, B	608	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: ade2, adeC, AGR_L_883, Atu4426 EC: 3.5.4.2
UniProt
Find proteins for Q7CUX4 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CUX4 Go to UniProtKB: Q7CUX4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7CUX4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.287
R-Value Work: 0.185
R-Value Observed: 0.190
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.662	α = 90
b = 131.845	β = 97.04
c = 69.628	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-11-02

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2011-11-02
Type: Initial release
Version 1.1: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection

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3T81

Crystal Structure of diiron adenine deaminase

Crystal Structure of diiron adenine deaminase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)